rapgreen

Class TreeReader

java.lang.Object

rapgreen.TreeReader

public class TreeReader
extends java.lang.Object

Tree file reading class.

This class contains file reading tools, to preformat file.

Field Summary

Fields

Modifier and Type	Field and Description
static int	NEWICK Newick format.
static int	NEWICKTITLED Newick format.
static int	SIMPLE Simple output
int	treeIndex The index
java.util.Vector	trees Trees
static int	XML XML format.

Constructor Summary

Constructors

Constructor and Description
TreeReader(java.io.File file, int format) Generic constructor, from several formats
TreeReader(java.io.File file, SpeciesDictionary dico, java.util.Hashtable index, int format) Generic constructor, from several formats, filling a species dictionary, and an ID index
TreeReader(java.io.File file, SpeciesDictionary dico, java.util.Hashtable index, int format, int output) Generic constructor, from several formats, filling a species dictionary, and an ID index
TreeReader(java.io.File file, SpeciesDictionary dico, int format) Generic constructor, from several formats, filling a species dictionary

Method Summary

Methods

Modifier and Type	Method and Description
Tree	nextTree() Return the next tree
int	toNewick(int index, java.lang.String source, java.lang.StringBuffer res, SpeciesDictionary dico) Private parser of a node, from a starting point in a newick string, to an ending point returned in an Integer object.
int	toSimpleNewick(int index, java.lang.String source, java.lang.StringBuffer res, SpeciesDictionary dico) Private parser of a node, from a starting point in a newick string, to an ending point returned in an Integer object.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NEWICK

public static final int NEWICK

Newick format. The newick file may contain several trees.

See Also:

Constant Field Values

XML

public static final int XML

XML format. The XML file is supposed to contain only one tree.

See Also:

Constant Field Values

NEWICKTITLED

public static final int NEWICKTITLED

Newick format. With title at the begining of the tree.

See Also:

Constant Field Values

SIMPLE

public static final int SIMPLE

Simple output

See Also:

Constant Field Values

trees

public java.util.Vector trees

Trees

treeIndex

public int treeIndex

The index

Constructor Detail

TreeReader

public TreeReader(java.io.File file,
          int format)

Generic constructor, from several formats

Parameters:

file - The tree file

format - The encoding format

TreeReader

public TreeReader(java.io.File file,
          SpeciesDictionary dico,
          int format)

Generic constructor, from several formats, filling a species dictionary

Parameters:

file - The tree file

dico - The species dictionary to fill

format - The encoding format

TreeReader

public TreeReader(java.io.File file,
          SpeciesDictionary dico,
          java.util.Hashtable index,
          int format)

Generic constructor, from several formats, filling a species dictionary, and an ID index

Parameters:

file - The tree file

dico - The species dictionary to fill

index - ID index to fill

format - The encoding format

TreeReader

public TreeReader(java.io.File file,
          SpeciesDictionary dico,
          java.util.Hashtable index,
          int format,
          int output)

Generic constructor, from several formats, filling a species dictionary, and an ID index

Parameters:

file - The tree file

dico - The species dictionary to fill

index - ID index to fill

format - The encoding format

Method Detail

toNewick

public int toNewick(int index,
           java.lang.String source,
           java.lang.StringBuffer res,
           SpeciesDictionary dico)

Private parser of a node, from a starting point in a newick string, to an ending point returned in an Integer object.

Parameters:

index - The starting index in the newick string

source - The newick string, encoding the information

res - The buffer used to return the result

dico - The species dictionary to fill

Returns:

The new index

toSimpleNewick

public int toSimpleNewick(int index,
                 java.lang.String source,
                 java.lang.StringBuffer res,
                 SpeciesDictionary dico)

Private parser of a node, from a starting point in a newick string, to an ending point returned in an Integer object. Produce simplified newick, containing only taxa

Parameters:

index - The starting index in the newick string

source - The newick string, encoding the information

res - The buffer used to return the result

dico - The species dictionary to fill

Returns:

The new index

nextTree

public Tree nextTree()

Return the next tree

Returns:

The next tree